Monday, September 14, 2009

The first genetic link in the evolution of the heart from three-chambered to four-chambered has been found, illuminating part of the puzzle of how birds and mammals became warm-blooded.

Frogs have a three-chambered heart. It consists of two atria and one ventricle. As the right side of a frog's heart receives deoxygenated blood from the body, and the left side receives freshly oxygenated blood from the lungs, the two streams of blood mix together in the ventricle, sending out a concoction that is not fully oxygenated to the rest of the frog's body.

Turtles are a curious transition--they still have three chambers, but a wall, or septum is beginning to form in the single ventricle. This change affords the turtle's body blood that is slightly richer in oxygen than the frog's.

Birds and mammals, however, have a fully septated ventricle--a bona fide four-chambered heart. This configuration ensures the separation of low-pressure circulation to the lungs, and high-pressure pumping into the rest of the body.

As warm-blooded animals, we use a lot of energy and therefore need a great supply of oxygen for our activities. Thanks to our four-chambered heart, we are at an evolutionary advantage: we're able to roam, hunt and hide even in the cold of night, or the chill of winter.

But not all humans are so lucky to have an intact, four-chambered heart. At one or two percent, congenital heart disease is the most common birth defect. And a large portion of that is due to VSD, or ventricular septum defects. The condition is frequently correctable with surgery.

Benoit Bruneau of the Gladstone Institute of Cardiovascular Disease has honed into the molecular forces at work. In particular, he studies the transcription factor, Tbx5, in early stages of embryological development. He calls Tbx5 "a master regulator of the heart."

Scott Gilbert of Swarthmore College and Juli Wade of Michigan State University study evolutionary developmental biology of turtles and anole lizards respectively. When Bruneau teamed up with them, he was able to examine a wide evolutionary spectrum of animals. He found that in the cold-blooded, Tbx5 is expressed uniformly throughout the forming heart's wall. In contrast, warm-blooded embryos show the protein very clearly restricted to the left side of the ventricle. It is this restriction that allows for the separation between right and left ventricle.

Interestingly, in the turtle, a transitional animal anatomically--with a three-chambered, incompletely septated heart, the molecular signature is transitional as well. A higher concentration of Tbx5 is found on the left side of the heart, gradually dissipating towards the right.

Bruneau concludes: "The great thing about looking backwards like we've done with reptilian evolution is that it gives us a really good handle on how we can now look forward and try to understand how a protein like Tbx5 is involved in forming the heart and how in the case of congenital heart disease its function is impaired."

The journal Nature reports the finding in its Sept. 3 issue. The National Science Foundation supports the research.

Stanford photo scientists are out to reinvent digital photography with the introduction of an open-source digital camera, which will give programmers around the world the chance to create software that will teach cameras new tricks.

If the technology catches on, camera performance will be no longer be limited by the software that comes pre-installed by the manufacturer. Virtually all the features of the Stanford camera – focus, exposure, shutter speed, flash, etc. – are at the command of software that can be created by inspired programmers anywhere. “The premise of the project is to build a camera that is open source,” said computer science professor Marc Levoy.

Computer science graduate student Andrew Adams, who helped design the prototype of the Stanford camera (dubbed Frankencamera,) imagines a future where consumers download applications to their open-platform cameras the way Apple apps are downloaded to iPhones today. When the camera’s operating software is made available publicly, perhaps a year from now, users will be able to continuously improve it, along the open-source model of the Linux operating system for computers or the Mozilla Firefox web browser.

From there, the sky’s the limit. Programmers will have the freedom to experiment with new ways of tuning the camera’s response to light and motion, adding their own algorithms to process the raw images in innovative ways.

Levoy’s plan is to develop and manufacture the “Frankencamera” as a platform that will first be available at minimal cost to fellow computational photography researchers. In the young field of computational photography, which Levoy helped establish, researchers use optics benches, imaging chips, computers and software to develop techniques and algorithms to enhance and extend photography. This work, however, is bound to the lab. Frankencamera would give researchers the means to take their experiments into the studios, the landscapes, and the stadiums.

For example, among the most mature ideas in the field of computational photography is the idea of extending a camera’s “dynamic range,” or its ability to handle a wide range of lighting in a single frame. The process of high-dynamic-range imaging is to capture pictures of the same scene with different exposures and then to combine them into a composite image in which every pixel is optimally lit. Until now, this trick could be done only with images in computers. Levoy wants cameras to do this right at the scene, on demand. Although the algorithms are very well understood, no commercial cameras do this today. But Frankencamera does.

Another algorithm that researchers have achieved in the lab, but no commercial camera allows, is enhancing the resolution of videos with high-resolution still photographs. While a camera is gathering low-resolution video at 30 frames a second, it could also periodically take a high-resolution still image. The extra information in the still could then be recombined by an algorithm into each video frame. Levoy and his students plan to implement that on Frankencamera, too.

Yet another idea is to have the camera communicate with computers on a network, such as a photo-hosting service on the Web. Imagine, Levoy says, if the camera could analyze highly-rated pictures of a subject in an online gallery before snapping the shutter for another portrait of the same subject. The camera could then offer advice (or just automatically decide) on the settings that will best replicate the same skin tone or shading. By communicating with the network, the camera could avoid taking a ghastly picture.

Of course users with Frankencameras would not be constrained by what is already known. They’d be free to discover and experiment with all kinds of other operations that might yield innovative results because they’d have total control.

"Some cameras have software development kits that let you hook up a camera with a USB cable and tell it to set the exposure to this, the shutter speed to that, and take a picture, but that’s not what we’re talking about," says Levoy. "What we’re talking about is, tell it what to do on the next microsecond in a metering algorithm or an autofocusing algorithm, or fire the flash, focus a little differently and then fire the flash again — things you can’t program a commercial camera to do."

To create an open-source camera, Levoy and the group cobbled together a number of different parts: the motherboard, per se, is a Texas Instruments "system on a chip" running Linux with image and general processors and a small LCD screen. The imaging chip is taken from a Nokia N95 cell phone, and the lenses are off-the-shelf Canon lenses, but they are combined with actuators to give the camera its fine-tuned software control. The body is custom made at Stanford. The project has benefited from the support of Nokia, Adobe Systems, Kodak, and Hewlett-Packard. HP recently gave graduate student David Jacobs a three-year fellowship to support his work on the project. Kodak, meanwhile, supports student Eddy Talvala.

Within about a year, after the camera is developed to his satisfaction, Levoy hopes to have to have the funding and the arrangements in place for an outside manufacturer to produce them in quantity, ideally for less than $1,000. Levoy would then provide them at cost to colleagues and their students at other universities.

The son, grandson, and great-grandson of opticians, Levoy sees his mission as not only advancing research in computational photography, but also imbuing new students with enthusiasm for technology. This spring he launched a course in digital photography in which he integrated the science of optics and algorithms and the history of photography’s social significance with lessons in photographic technique.

As many ideas as Levoy’s team may want to implement on the camera, the real goal is to enable the broader community of photography researchers and enthusiasts to contribute ideas the Stanford group has not imagined. The success of Camera 2.0 will be measured by how many new capabilities the community can add to collective understanding of what’s possible in photography.

Potted plants add a certain aesthetic value to homes and offices, bringing a touch of nature to indoor spaces. It has also been shown that many common house plants have the ability to remove volatile organic compounds—gases or vapors emitted by solids and liquids that may have adverse short- and long-term health effects on humans and animals—from indoor air. But take heed when considering adding some green to your environment; in addition to giving off healthy oxygen and sucking out harmful VOCs, a new study shows that some indoor plants actually release volatile organic compounds into the environment.

A research team headed by Stanley J. Kays of the University of Georgia's Department of Horticulture conducted a study to identify and measure the amounts of volatile organic compounds (VOCs) emitted by four popular indoor potted plant species. The study, published in the American Society for Horticultural Science journal HortScience, also noted the source of VOCs and differences in emission rates between day and night.

The four plants used in the study were Peace Lily (Spathiphyllum wallisii Regel), Snake Plant (Sansevieria trifasciata Prain), Weeping Fig (Ficus benjamina L.), and Areca Palm (Chrysalidocarpus lutescens Wendl.). Samples of each plant were placed in glass containers with inlet ports connected to charcoal filters to supply purified air and outlet ports connected to traps where volatile emissions were measured. The results were compared to empty containers to verify the absence of contaminants. A total of 23 volatile compounds were found in Peace Lily, 16 in Areca Palm, 13 in Weeping Fig, and 12 in Snake Plant. Some of the VOCs are ingredients in pesticides applied to several species during the production phase.

Other VOCs released did not come from the plant itself, but rather the micro-organisms living in the soil. "Although micro-organisms in the media have been shown to be important in the removal of volatile air pollutants, they also release volatiles into the atmosphere", Kays stated. Furthermore, 11 of the VOCs came from the plastic pots containing the plants. Several of these VOCs are known to negatively affect animals.

Interestingly, VOC emission rates were higher during the day than at night in all of the species, and all classes of emissions were higher in the day than at night. The presence of light along with many other factors effect synthesis, which determines the rate of release.

The study concluded that "while ornamental plants are known to remove certain VOCs, they also emit a variety of VOCs, some of which are known to be biologically active. The longevity of these compounds has not been adequately studied, and the impact of these compounds on humans is unknown."